Aquifer vulnerability assessment constitutes a crucial tool for the protection and sustainable management of groundwater resources, particularly in complex karst aquifers. This study conducted a detailed comparative analysis of two tailored and widely used vulnerability mapping methodologies, COP and PaPRIKa, to evaluate their performance within a Mediterranean karst groundwater system. The methods were employed for the development of a hybrid vulnerability map after geospatial and statistical analysis. Both COP and PaPRIKa were applied using a combination of geological, hydrological, and geomorphological aquifer characteristics that can potentially influence its vulnerability to contamination. While COP predominantly assigned Low and Very Low vulnerability values across the study area, PaPRIKa identified the Moderate class as dominant, suggesting a finer sensitivity to karst-specific features. To address potential biases in PaPRIKa, a single-parameter sensitivity analysis was performed, leading to adjusted weights and the development of a modified version, PaPRIKa-Mod. A quantitative comparison of all three methods highlighted the varying degrees of consensus and discord, with PaPRIKa and its modification showing the highest consistency, suggesting robust methodological integrity. Conversely, the comparison of COP with either version of PaPRIKa revealed a lesser yet notable concordance, underscoring their capacity to be integrated and their potential to complement each other in vulnerability assessments. Finally, a hybrid vulnerability map was developed from the integration of similar vulnerability classes, attributing the most vulnerable setting prevailing across all methods. The methodological approach that was followed is adaptable and can provide significant insights for vulnerability estimations across different regions and methodological concepts.